The Secret War
by grifan526
Summary: Takes place after Revolutions. Problems arise that could destroy the pact between machines and humans or cause them to combine forces.
1. Chapter 1

Disclaimer

I do not own any characters from the Matrix that are in this story. The rights go to the Wachowski and Warner Bros

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Chapter I

He slowly opened his eyes realizing his whole body ached with the pains from the battle he just fought. Neo slowly sat up groaning as he did so. He looked around to find out where he was and quickly recognized his surroundings.

"Oh, shit. How did I get here again?" He said as he painstakingly walked over to the benches to sit down.

Once again Neo has woken up in the train station joining the Matrix and the machine world. He sat staring at the familiar white walls and the room in which he could never escape without help from the trainman.

He sat for nearly an hour trying to figure out how he had gotten here from the machine city and wondering if the battle with Smith really happened. After seeing that this was all real, he closed his eyes and began to try and concentrate on finding a way out of this plain dismal place. As he attempted tears began to streak his face and his face fell into his hands as he began to sob. After only a few sobs he lifted he began to mumble Trinity's name.

"She is really dead this time. I can't save her. What is the fucking point of being 'the One' if I can't do a single damn thing worth while? I am never going to get out of this shit hole and even if I did there is no point in going." He turned and grabbed a nearby man by him by his shoulders and screamed in his face. "What is the fucking point?" he paused for a second and released the man and backed up. "Holy shit. Seraph, how the hell did you get here?"

"I brought the train. Oracle told me to come."

"How are you both alive?"

"Come, she will explain it all."

Very happy, but very confused Neo got onto the train that he never heard or noticed arrive over his great outcry. "Trinity is dead, and now I wish I was. I did all of this for her, and now it was all a waste." Neo said very calmly staring at the wall.

"I am deeply sorry, I know how much she meant to you. I can assure you though, none of your actions were in vain, much has changed and much still needs to be changed. If you don't mind, please tell me of what happened since our last meeting."

Neo began to explain his trip into the machine city and the fight with Agent Smith. He told about how Bane had blinded him and was also somehow infected by Smith. He also detailed the way he saw the evasion of the city defenses and the fall into the city, followed by Trinity's death, which he paused after. He then told of the pact he made with the Source and the final battle between him and Smith. After finishing he realized how much time had passed and look at Seraph. "How long is this train trip? I don't remember it being this long."

"We are not going to the same station as before this, one is much further, but we are arriving now."

Neo looked out the window noticing the familiar light of the train stations that he had seen so many times. Him and Seraph walked through the crowd of people up to the street level. "My God, they have no idea what has happened to them these past few days do they?" Neo said looking at Seraph. " No, they know nothing, the Source made sure of it so there would not be any unneeded commotion. The problem is not everyone forgot, and that is where we are having the problem."

They walked a couple blocks until coming to an apartment building that Seraph pointed out was the one that the Oracle now lived in. They went in and went to her room where Neo was greeted with the familiar smell of cookies.

"I finished them this time for you Neo." Oracle said from the kitchen where she was putting the cookies onto a plate for him. "Come and sit, I know you have a lot of questions and I will try to answer the ones that I can."

Neo sat and picked up a cookie and looked at it as he started talking slowly shifting his gaze towards the Oracle. "Why am I here, I thought I was destroyed after the fight with Smith? Isn't that what is supposed to happen once I enter the Source?"

The Oracle looked away from him with a look of contemplation as she lifted her finger as to make a point. "That is a very interesting question with a very interesting answer. What seems to have happened, is that with the power the Source sent through your body was strong enough that it imprinted you into a new program file making a copy of you that is actually able to survive in the Matrix, even without your real body being alive. To answer your next question you ended up in the train station because just like last time you felt the source in a way you were not ready for and were sent to the train station, but this time, more like new program entering the Matrix from the machine world."

"Wait, are you trying to tell me that I am a program?" Neo said with a strong air of confusion.

"Yes, that is exactly what I am trying to tell you?

"So I am no longer human? I am now a machine?" Neo said with more rage than confusion now.

"Well, you are more of a human, in machine language. The body is merely a vessel for the true essence of a human, which is the mind. But if you no longer wish to see yourself as human just because you lack a body, then so be it ,but it will be much more comforting to accept that you are still human in ever essence. There is nothing different from you now then before, just where the signal comes from. And with this being said I imagine you are starving."

Neo realized that he was in fact extremely hungry. "I am, but will food even matter, I don't need it?"

"Well, the mind controls whether or not you are hungry, and it is going to react just the same as it always has, so you should eat something. What would you like? How about a sandwich?"

Still absorbing this massive amount of information, Neo said yes very blankly and emotionless. The Oracle made a couple of sandwiches and they sat and ate in a silence that seemed filled with thought. It was finally broken by Neo, when he looked up and asked "Can I still alter things to my wishing?" The Oracle merely pointed in response, to the sign that always seems to be over the door the says " Temet Nosce" meaning "Know thyself".

"Of course, only I can answer that." He said as he looked at his hands, and then his surrounding environment. He then looked at the table with the dirty dishes and looked up at the Oracle, "How about I do the dishes?" Neo then made all the leftover food scraps disappear, then the dishes floated up to their places in the cabinets. As he finished, he looked to his old friend, and they both smiled in amusement and joy.

"You always did use your power for good." Oracle said smiling at him with a sense of wonder. "I would imagine that now that you have entered the source and were altered by him, you can change the Matrix even more than before. I don't know by how much, but I am just saying there may be more to you now than ever."

Neo sat looking quietly at her knowing that it is really pointless to try and continue asking about this subject knowing she would never be able to answer him, only he could do that. As he sat thinking for a few seconds he got up and walked over to the window. Leaning against the wall and looking out at the people still living in the Matrix. "What has happened now that there is a pact between the humans and machines?"

"I was waiting for that question to arise. Many programs have been altered and deleted, so much so, that you could almost say we are now in the fourth version of the Matrix. This one is not so much a method of control but one just here to hold humans in place so that there can be power generated. There are no longer agents to keep people from leaving, but agents to keep the peace, and monitor programs and exiles. From what I have heard these new agents can even delete any program that is acting as it shouldn't, which can be quite scary for many of us exiles." At this Neo looked up at her and interrupted her in confusion and needing clarification.

"By saying "us exiles" do you mean that, you are an exile now?"

"Yes, I am no longer need as a form of control to make sure that the cycle of the one continues, being you have now ended the war. Seraph is too, being without me there is no need for a protector of me. Very few programs did not choose exile, and that leaves a small problem being, there are now many unregulated programs searching for a place to fit in, most have gone to join the Marivingian." She said this name with a tone of disgust, being she despises his very way of living and control.

Neo looked shocked at the sound of the name of a past enemy, and a man he strongly loathed. "He is still here! I am sure up to no good, isn't he?"

"You got that right kid, no good at all. He wants to control the Matrix, become the ruler of all the humans, and destroy the ones who are unplugged. I would not be surprised if he wants his power to spread through the machine world either. Unfortunately, the source can't stop him directly being he is an exile, but that is where you come in."

"I knew there had to be a reason you wanted to talk to me. Why can't it ever be to just reminisce about old times." Neo smiled, giving a sense of humor and that he was feeling better, after absorbing the massive amount of information.

"I know, I'm sorry Neo, but you are the only one capable of stopping him from spreading further. He has become, a kind of mob leader among many exiles, and many humans. Of corse there are many things he wants, and needs to be able to spread as far as he is planning. One of those is you." Neo looked at her in a way seeming displeased at this news but not at all surprised.

"He wants me for my power I am sure, but there is no way for him to get, right? And even so, how am I suppose to stop him?"

"You have the power to stop him, but he has many guards, and many of them are exiles some are even old assassins from the Source…"

"What do you mean assassins?"

"Once programs started becoming exiles and doing what they weren't supposed to be doing, another program was created to assassinate them. They are basically programs made to delete other programs. Once some of them became exiles, it became very hard to get rid of them, and so many of them have survived throughout the years working for various underground programs and men as hit men."

"An obvious question is, can they kill humans?"

"Oh yes, they can do it the conventional way with a gun, or using there assassination power which damages their brain at the least, or possibly severs the connection with the Matrix that they had, making them brain dead. These are the ones you want to watch out for, even they can kill you if they got the chance, and many are extremely hard to kill."

She paused for a minute to let all of this sink in, and to allow for Neo to think about it. He began to think how easy it was to take on missions against programs when he worked with other people who were hacked in and could manipulate the Matrix just like the programs. He knew that he would need help to get through this, but only the freed people would be of any help. This brought up a question and out of the odd silence he asked her abruptly, " Is there any way to contact Zion? It would be very helpful if I could work with some old friends on this one."

The Oracle shook her head as she began to answer him, "No, not directly, the only way is to contact a hovercraft as I have done often, or one of the people who are hacked in."

"Well, how do we do it? How do we contact a ship?" Neo said very excited.

Well we can send a signal out and see if any ships are in the broadcast range, and you can keep an eye out for any hackers, but that is the best we can do."

Still very excited Neo replied sounding almost rushed, "Ok then, let's do it, and how do we exactly?"

"It is a function built into my programming, to be able to access to communication lines and contact Zion's ships. Now, what would you like it to say being you know these people the best?"

"Just have it say you want to contact either Morpheus or Niobe about important matters within the Matrix. I am sure Morpheus has gotten himself into trouble with all the rules he broke, so I only expect Niobe will be able to come."

The Oracle sat and closed her eyes making a face showing that she was deeply concentrated, and that there was something going on in her mind. Neo sat and watched with great anticipation, waiting for her to speak with some kind of assurance that the signal has been received. The Oracle opened her eyes and told that the signal was sent and they could only wait.

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Thank you from reading my story. Please send me a review and if it is critism please don't be too harsh but it is welcome. I will try to update as much as possible but with school don't expect more than a chapter a week- thanks Grif


	2. Chapter 2

Chapter II

After the war, Zion started looking for places near the surface to began moving back to the old way of life. Many believed it advantageous to move to the surface, at least then there was growing room and the possibility of mining operations. There would be new jobs for everyone who wanted them and Zion could leave their form of dark ages caused by the war. Also with the city on the surface broadcast range would always be there and people would be free to move in and out of the Matrix, and freed minds could easily be taken out and helped to be adapted to their new way of life. With this new idea, a hovercraft's main job was to search for a new place for settlement.

The _Hammer _was the first hover craft to be repaired and begin these routine missions. Their mission was to search for a settlement area and to enter the Matrix and try to spread the word of the Real World. This talk gave them more criticism than cooperation and very few minds were freed.

"So Link, anything interesting going on in there?" Niobe asked in a very nonchalant way, showing that she was bored with the lack of action.

"Nope, all very routine. Just people walking around and going through their normal lives." Link replied with the same tone of boredom and looked at Niobe with a look that he too missed the excitement. "There are times, I wish we didn't end the war. Now, everything has become, well, routine, with very little excitement." He turned away from Niobe, back towards the screens of falling green symbols of the Matrix. "I wish Neo was still here, it was so amazing to watch… what the hell! Niobe check this out."

The both stared at the screen noticing familiar, but impossible symbols. One of the screens beeped showing that there was an incoming transmission. "Why the hell would Oracle be sending us something?" Niobe said, seeing who the message was from. "Why the hell does she want to see me? Unless… Link, can you verify that those symbols are Neo?"

"Yea, just give me a sec." Link began typing onto one of the various screen and came up with the answer for Niobe. "It most certainly is, you gonna go in, or are you going to contact Morpheus?. The message did ask for both of you."

"No, I'll go in, besides Morpheus is busy in Zion getting all that shit sorted out." Niobe began to walk away to get Ghost so they could go in and see what the message was about. "Link, Oracle is with Neo right?" Link nodded in response still staring at the screen trying to figure out what was going on. "That son-of-a-bitch, he's been alive for these past three weeks and hasn't told anybody. Won't Morpheus be happy though."

Niobe and Ghost laid down into their seats where Link jacked them into the Matrix only a few streets away from where Neo was staying in New York City. They walked through the crowds of people until they reached the apartment that Neo and Oracle were staying in, and walked to the door that had brass numbers 303. Before they knocked Seraph opened the door letting them in. "Please, come in. We have been waiting for you." He held the door open slightly bowing his head as he stretched out an open palm as if showing them the way in.

Niobe and Ghost walked into the living room where they saw Neo sitting on a couch watching a show on tv and they could hear the Oracle in the kitchen. Neo looked over at them with a wide smile showing his great joy in seeing them.

"You piece of shit." Niobe said to him with a small smile.

"Glad to see you too," Neo said as individually grabbed their hands and patted their backs. "I was beginning to wonder if my message was ever going to be answered. Where is Morpheus? In the stocks."

"No, his trial was postponed until the city was rebuilt, or at least functional. It was just recently announce that it will be in two weeks." Niobe responded. "But none of that matters. You had best tell us what you are doing here, and why you called for us."

Neo explained the best he could about how he got into the current situation of being a program and then explained about the battle going on inside the Matrix. He paused and looked at Niobe and Ghost with a look showing that he realized he did not know a vital piece of information. "I have not heard exactly what the pact was between the machines and Zion."

Niobe looked at him slightly raising her eyebrows but keeping her face in a position of stone. She then looked down and shook her head as she began to tell what happened, "Well, I've got to say it was some weird shit. Some sentinels and a different kind of machine came down to the city. The new machine looked almost like a spider with all these arms and eyes but his head was kinda like the sentinels. The craziest part was how we just let them come in like that. Well, the new machine it turns out was a delegate from the machine city and him and the counsel had a meeting and worked out a treaty. The rules are, any aggression on either side will be taken as an act of war and they will come to destroy us once more. We are can unplug people from the Matrix as we wish as long as they choose to be. Their agents will not attack us under any situation unless we commit an act of war. We can also freely move from city to city. So all and all, it came to don't piss with us we won't piss with you."

Neo nodded his head in understanding and had a look in his eyes of thinking before he looked at his old friends to tell them his plan. "Well, that is good. My plans will not interfere with the pact."

"What are these plans of yours exactly?"

"Well, first we need to start and underground movement to spread out information about the real world. We need to start freeing minds that is for sure, but it is not the main thing that needs to be done. As I have told you the Marivingian has already started to gain power and quickly, he must be stopped. I need as many people from Zion who are already used to fighting in the Matrix to join me and try to destroy this man. There are many programs working for him that are going to be hard to get through. I need you to get as much help as possible from Zion and I will go and get intel on what we are up against. I am not going to do this if I can not be sure that you are with me in this."

"Hell yea I'm with you on this. I would love to get back to fighting. these missions we have been on are driving me nuts. Yea, I get to fly a lot but, I love fighting too, and simulations just aren't cutting it anymore." Niobe looked at Ghost who nodded in return showing that he knew what his partner was thinking. "We will see what we can do in Zion and get back to you. If at all possible we will bring Morpheus with us. Now how are we going to contact you when we need to?"

"I will be going to San Francisco to join our old friend. I will send you my number there right before you leave so you can call me when you are ready to get this started."

"That's great. We will get back to you after Morpheus' trial. I know it is a few weeks away, but it is going to take time to get your army."

"It doesn't have to be too many. I just need back up. But that is a good time, I should have learned enough by then."

"You know, it is good seeing you again Neo. I know Morpheus will be glad to hear that you are alive. We'll call you in a few weeks." Niobe and Ghost looked at each other and walked out of the apartment and went down the street to the same place that they had entered the Matrix to leave.

Neo watched them walk down the street from his window. When they had left his sight he walked over to Seraph. "Are you ready?"

"I am. I will get Oracle, and we can go." Seraph went into the kitchen and came back with Oracle. He pulled his many keys from his sleeve and put one in to the closed door, turned his key and opened the door showing the hall of doors that could move them to many places within the Matrix.

The three programs entered the hallway, and walked down the white corridor and stopped in front of one of the many green doors. "This one should be good" Seraph said has he pulled out his key once more and opened the door.

They walked into another apartment this time one in San Francisco. It was very plain and empty. The walls were a tannish-yellow and there was the same color shag carpet. "Well Seraph, it's not the nicest place you've picked out but it will do." Oracle said looking around her new apartment, but sounding a little sad.

"I wouldn't say that." Neo said smiling at her. "Tell me how you want it and I will do it." This was followed by a laugh from Oracle and Seraph just smiled. Oracle had Neo make the apartment look just like her old one from when Neo first met her. To follow through with his plan Neo contacted Niobe in order to give her his new number and address.

Neo walked to the roof top of his new home to get a view of the city and to search for any anomalies that could give away the Marivingian and what he is up to. He looked at the city for hours until night admiring the view and searching for anything that could be interesting for him to do. As he waited Seraph came up to see him and to find out what he was doing.

"Hello Neo, it is a nice view isn't it?"

"Yea, I guess so. I never really looked at it before, this is first time I actually took time to see it, I can't help but think it is all a load of shit." Neo said never looking away from the city view.

"It does make you wonder though, is this what it was really like, is this how the human cities really looked." Seraph said as he walked over to stand by Neo and look with him.

Neo turned his head and his body soon following towards Seraph. "You do have a point. I guess, I am still trying to get used to my new life. I never spent much time there, but I really miss Zion." As he continued Neo began to smile as he thought of his old home. "It's true what they say, that you never know what you had until it is gone. I just hope nothing happens to Zion, I hope this little war that is about to start doesn't spread there as well."

"Yes, that would be unfortunate. What exactly do you have planned?" Seraph asked with a look of interest.

"Well, tonight I am going to fly over to his tower, and his country home, to see what I can see. I want to know what we are up against and how many people from Zion I need. After that, I will be able to start making a plan for attack."

"It is interesting to see how your mind works. I also think it will be interesting to see how you work in this situation, being I have never fought along side of you." Seraph and Neo exchanged looks after this, and Seraph knew it was time for Neo to go on his reconnaissance mission. Seraph nodded in response and walked back towards the stairwell. Neo crouched down and shot up into the air as Seraph watched this amazing feat for the first time.

He flew across the city to the large office building where he had met the Marivingian and knew that he did many things from and examined it and the code from it. The building appeared empty, but he could see a complex working of underground tunnels and rooms, and that is where Neo figured he held the mob operations.

Not finding what he wanted, Neo flew to the outer city, where Marivingian's closest estate was to look for any activity. This estate was nearly fifty acres surrounded by forest. The acre that the mansion was on, was all grass with the scattered flower beds and a path that wound through them all around the house. The actually building was three stories with nearly one hundred and fifty rooms that Neo could count. It was a tan stone with red barrel shingles and intricate work done around all the many windows. It was an architectural and artistic masterpiece that would be appealing to any eye that laid upon it and showed the wealth of the owner, just as Marivingian would want.

This new looking ground was an anthill of activity. Neo counted close to one hundred exile programs in this estate. He saw Marivingian and Persephone in the center room of the whole house talking to a few men. There were five programs patrolling the perimeter and four dogs. None of these looked familiar to Neo, none of them had the appearance of being normal programs and he was unable to tell what their functions were.

Neo could tell there were many programs here that he was unable to identify. Either they were too old for him to read or they had altered themselves in some way. Even Marivingian was different, he still had the same construct coding, so Neo was able to identify that much code, but there was a change in the function code that was written in to him. Neo could not tell what it was but he knew it was not good. The same twins where still there unchanged only feet from their master watching all that came near him and that were in view of the room. Neo had seen all he needed to know that this mission was going to be very difficult and that he needed as much help as he could get. He was beginning to think he may even need to call on help from the new agents.

Neo flew back towards the city to return to the apartment in which he now lived. He stopped a few streets away wanting to walk down familiar ground and to try and take in the fact that this was his new home and their was no returning. The city was unchanged, people walking everywhere, stores closing as it got late and others opening for the night life they supported. The great crowd of people that Neo could not only see, but feel the presence of, a presence that he knew was the control over them, that he was determined to break and free humanity for real now.

He turned down an alley to get onto the street he needed to be on, and as he walked through it, a chill went down his back and he turned at the feeling of somebody behind him.

"Hello Neo" The man said. This man was about the same height as Neo and had short ragged brown hair. He was dressed in a looses trench coat and was completely clothed in black. He almost seemed like he was another person from Zion.

"Who are you? Do I know you?" Neo said with no sound of emotion in his voice even though he was very unsure about this new person. All he could tell was that he was a program and none that he recognized.

"No, you do not know me. And just to humor you my name is Scar, at least that is what my comrades have deemed me. The man slowly walked towards Neo as he said this holding his hands out to show that he was no threat. "I have come to see you Neo I have business that needs to be dealt with you in private."

"What kind of business?" Neo said now showing a bit of confusion and caution in his voice.

"My business with you," Scar said taking one more step towards Neo putting him within arms reach, "is deletion." Scar suddenly thrust his hand flat out against Neo's chest.

Neo froze for a second as he felt his whole body feel alive with electricity. His image began to ripple, making him seem like a ghost. Spreading away from Scar's palm the appearance gave away to the coding that makes up Neo. Neo soon became terrified as he realized he could not push this back the way he did when Smith tried to copy himself onto Neo.

Neo reached out with both arms to grab Scars one. He froze for a second after this in pain, then Neo forced himself back pushing away from his adversary and kicking him in the chest. This threw Scar back across the alley into the side of a dumpster bending it in. Neo fell back doubled over, as his coding returned to normal making his appearance as it always was. Once the pain subsided Neo stood up straight watching his new foe get up and walk back towards his target.

"I see that this is going to be tougher than normal. Good, I could use a good challenge once more." He ran towards Neo throwing his fist out towards Neo's face as soon as he came closer.

Neo blocked it with the side of his arm and punched with his other arm and this punch was also blocked, but now Scar was blocking. Knowing this was going to happen Neo threw up his knee into his opponent pushing himself off of Scar so he flew back into a flip. He landed and ran at Scar kicking at his head. Scar ducked and sent an uppercut into Neo's stomach causing him to double over and fall on the ground as he lost balance. Before scar could react to his victims weakness Neo got onto his hands and grabbed Scar's head with his legs. He used this new position to pull himself quickly over Scar's head and throwing Scar into the ground in front of him as Neo continued his flip over Scar.

Scar landed hard, making a crater in the ground. He slowly got up and looked at Neo, "Very good, you are a much stronger fighter than I predicted. I give you much respect but that won't save you from deletion. I have much prize if I return with you head." At the finish of his sentence he jumped into the air and flew nearly as high as the buildings surrounding him.

Neo watched and prepared for this aerial attack but could not do it well. Scar came down by Neo grabbing his arm that was out to deflect this attack, and using his weight to thrown Neo off balance and threw the wall next to them. Neo quickly gathered himself up and ran back at Scar for one last attempt. His opponent waiting for him began to throw a punch hoping to meet its target at the time he got there. Neo went under this hitting scar in the stomach with his shoulder and flipping him over him. As scar fell Neo ax kicked him to make the impact even harder. Another crater was created, but this time Scar grabbed Neo right as he hit the ground needing no time to gather himself. He pulled Neo down onto the ground and flew over him to attempt deletion once more while his target was down. Neo dodged the palm and Scar's hand hit the ground leaving a hole where the ground was deleted instead. Neo launched his leg at Scar's side throwing him back several feet and giving Neo the force need to get onto his feet quickly in a spin upwards.

Neo always knew when he was not ready to take on an opponent and he got that feeling once more. Neo hoping his new plan would work, put up his hand in front of him, to take advantage of his stronger ability, and caused the air to ripple with change, followed by coding which solidified into a large brick wall, trapping his opponent inside the alley. As Neo slowly walked away in pain, he turned to see a strange image on the wall. The image he soon noticed was caused by the rippling from Scar walking through the wall. Neo knew there was no escape and decided to run the only way he knew would work. Neo crouched and shot into the air to fly away.

He landed just down the street, after flying in a large circle hoping to mislead Scar, and walked inside his new apartment. He looked panicked up at Seraph and Oracle, "We have a big problem."

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the story is feeling a little better starting to flow at least I feel like it is. I hope it is becoming more enjoyable-thanks Grif 


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